Please don't take this as a flippant answer, but you can already make extensive notes outside of the software. I use Word and Excel, but even Notepad is enough, or pen and paper. I have limited programming time so it wouldn't be a high priority to replicate note-taking, apart from maybe adding a free text tab to fleets. A more involved, automated system would involve a considerable amount of work because of the variety of things that can happen in the game, especially with different context in many cases. It isn't something that has been requested before.
The game already has events to tell you when things finish, or when you have forgotten something like allocating research labs. You can read back through all the past events. You can also have your fleets send you a message when they arrive somewhere, reminding you of why you sent them. I know some people even create fake fleets, or 'message bots', to use the remind messages on a regular basis. It also helps to get into a regular routine - checking terraforming fleets, checking survey fleets, checking build queues, mining output, etc..
For the sentry buoys specifically, you can check where they are deployed on the Galactic Map, using the Missiles tab (assuming that is pre v2.6). I use that all the time to plan buoy placement.
It's your game, not mine, but all the solutions that you mentioned are symptoms of problems that the game has. These are hacks and workarounds that allow some players to overcome issues (like forgetting stuff) with some additional manual work. If you see players making bot fleets just to remember to do something, then perhaps they need better tools in the game so that they don't have to resort to hacks or create external resources like Excel sheets to keep track of what were they doing and what they plan to do. In the end, it's an additional stuff that you have to do, and is quite costly in terms of time, that you have to pay before you even start the new game. That's of course on top of having to design all the required ships and installations, what already takes a lot. Then you have to maintain those sheets, the more complex they are, the more time you have to spend maintaining them.
The game is great, don't get me wrong, but at some point it should start moving towards automation of things instead of relying on the player to do everything manually. Ideally you shouldn't have to check events log all the time just to make sure you didn't miss anything, because things should work when you set them up and only break if there was a third party introduced into the mix. Of course there are people who don't mind the hard work, but I don't think there are many of them. I'm not 100% sure that automated objectives would solve anything, maybe it's not such a great idea after all, who knows, but the fact that it wasn't requested before is not very surprising. Complex games tend to attract people who like them (I know, impossible:D) and these people take pride in overcoming design flaws that make games unplayable for the general public. I mean, who is going to complain about lack of organisational tools in the game that forces to you to select a target for every missile in the fleet of 20 ships, each capable to deploy more than a hundred at once. It seems like such a non issue in comparison.
I won't bother you with this anymore, just keep in mind that when players start using in game systems in a weird way, it's because they are missing something that wouldn't force them to jump through all those hoops to do something simple. Just because I can spend 10 minutes setting up fake fleets to remember about something in 20 minutes and do it again for 5 other things, doesn't mean it's fun and I'll be able to keep on top of it forever. Maybe instead, I just need a reminder function with simple text input that I can set up with 2 clicks and focus on something else. Or maybe I need something else, like an action that triggers at certain condition. It's hard to say without knowing specific cases, but making notes/using external software to deal with the game shouldn't be a go to answer because it will overload everyone at some point, be it sooner or later. Also, for every player that will use word/excel/set up fake fleets, there will always probably be 10 or more other players just will just bounce back from the game, never to return, not giving it a chance.
